Population Genetic Analysis Of Popular Hybrid Rice And Parental Lines In Recent Years

Rice?Oryza sativa L.?is an indispensable food in the world.In the past sixty years,rice breeding and production have experienced two major breakthroughs.One is the development of dwarf varieties,and the other is the creation and utilization of hybrid rice.These breakthroughs have more than tripled the level of rice production.At present,the breeding of hybrid rice has been very common,but the parental selection of hybrid rice still relies on large-scale random matching.How to improve the efficiency of hybrid breeding is an urgent problem.Finding out the general rules from commercial hybrid rice is expected to help answer this question.In this study,we collected 165hybrid rice varieties planted in large areas across the country in recent years,and obtained the genotypes of their parents using innovative strategies.Then,a series of analyses of parental lines was performed,including the population structure,selected sites,phenotype-associated loci and their effects in hybrids,aiming to providing useful information from a genomics perspective for hybrid rice breeding.The main results obtained in this study are as follows:1. Innovative method for obtaining parental genotype data of hybrid rice. We obtained genomic data of 165 hybrid rice varieties with a large promotion area from2011 to 2015.In addition,High-quality genomic DNA which was extracted from chaff was sequenced to obtain genomic data of maternal lines.Based on the corresponding relationship between F₁ and their maternal lines,the genotype of paternal lines was inferred.Twelve artificially constructed hybrid data were used to evaluate the extraction,imputing,and inference steps,and the correctness rate of the inferred paternal genotype is about 97%.Average missing rate of paternal lines'genotype is lower than 5%.After all,We got 6,684,955 SNPs and the density of SNPs is 17.9SNPs/kb.2. The population structure of parental lines was analyzed. The results showed that the paternal population was similar to the Indica II population,and the maternal population was similar to the Indica I.The paternal lines of three-line and two-line had no obvious intergroup boundaries,while the maternal lines of three-line and two-line were clearly clustered into two groups.The maternal lines of three-line were more similar to the Indica I group.The XP-CLR and fixation index?Fst?method was used to identify the selected loci between parents,including TMS5,Rf4 and other genes related to the characteristics of sterile lines and restorer lines.3. Genome-wide association study?GWAS?on the panicle phenotypes of the hybrid rice population. Whole-genome association analysis yielded 163 non-repeated association loci,and we analyzed the genetic effects of these association sites.We found that additive,dominant and super-dominant effects all contribute to heterosis.Significant intervals include cloned genes such as IPA1 and Ghd7.The effects of some cloned gene segments were analyzed.We calculated the specific heterozygosity of the material by using related sites.Compared with general heterozygosity,special heterozygosity has a stronger correlation with heterosis.4. Combined GWAS results with the parental lines analyses. Among the loci with allele frequency difference?AFD?greater than 0.4 between parental populations and significantly associated with panicle phenotypes.There were 72.2%of loci of which the advantageous allele frequency were more frequent in paternal populations.That indicated that the genotypes of the restorer lines had an important contribution to heterosis.5. Analyzed the selection of superior alleles in different breeding periods. Combining the core collection published by predecessors,the research materials will be divided into three breeding periods.The genotypes of the association loci obtained through GWAS in the three breeding periods were analyzed,and it was found that 30%of the superior alleles were positively selected during the breeding process.6. Analyzed parents of indica-japonica hybrid rice.The introgression of indica-japonica hybrid rice parents were obtained and compared with typical indica rice and typical japonica rice.It was found that the introgression of the indica-japonica hybrid rice parents accounted for a higher proportion of the whole genome than the typical indica rice and the typical japonica rice,and the location of the introgressed fragments of different materials had overlap.These introgressed fragments may be related to the fertile of indica-japonica hybrid rice.